Talk:20.109(S13):Phylogenetic analysis (Day7)

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General notes

I believe some groups are still in the process of reverse complementing inserts in the non-usual orientation.

Agi is in the process of trimming and analyzing four additional #709 clones prepped and sequenced yesterday -- looks as though only one will be good. I may not finish until after class today, circa 5 pm. Update: even later than that. I can do the final addition to an existing #709 .mas file if need be, also including samples from a student who has been ill.

Final sample-wide alignment files and trees

One representative from each sample-based group should post a .mas and .pdf file here when data are in final form. That way we'll all have quick access to the location sub-trees.


Sample # Alignment file (.mas) Tree file (.pdf)
702 Media: Final_702_Alignment.mas Media: Final_702_PhyloTree.pdf
709
712 Media: Final_712_Alignment.mas Media: Final_712_PhyloTree.pdf
716 No clones worked No clones worked
405
664
732
729

T/R microbiome

Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].

Team Color Team Member Gull ID Sequence 1 (txt) Sequence 2 (txt) Sequence 3 (txt) Sequence 4 (txt) Sequence 5 (txt) Sequence 6 (txt) Sequence 7 (txt) Sequence 8 (txt) Species overview (xlsx) Alignment (mas) Tree (pdf)
Red Nick 702 Media:TR-Red_702-C1.txt Media:TR-Red_702-C2.txt Media:TR-Red_702-C3.txt Media:TR-Red_702-C7.txt Media:TR-Red_702-C8.txt Media:TR-Red-Species.xlsx Media:TR-Red-Blue-702.mas Media:TR-Blue-Red-tree.pdf
Red
Orange Daphne, Stas 712 Media:TR-Orange_712-C2.txt Media:TR-Org_712-C5.txt Media:TR-Org_712-C7.txt Media:TR-Org_712-C8.txt Media:TR-Orange_712.xlsx Media:TR-712-Alignment.mas Media:TR-712-Alignment.pdf
Orange
Yellow Ebaa 664 Media: TR-Yellow_664-C1.txt Media: TR-Yellow_664-C4.txt Media: TR-Yellow_664-C8.txt Media: 664_S13-M1D7-template.xlsx Media: WFTR-664-alignment.mas Media: WFTR-664-tree.pdf
Yellow Dominique 739 (everything should be in correct seq order) Media: TR-Yellow_739-C2f.txt Media: TR-Yellow_739-C3.txt Media: TR-Yellow_739-C4f.txt Media: TR-Yellow_739-C5f.txt Media: TR-Yellow_739-C6f.txt Media: TR-Yellow_739-C7.txt Media: TR-Yellow_739-C8f.txt Media: 739_S13-M1D7-template.xlsx Alignment of all 739 from TR Media: TR-739-alignment.mas Alignment of TR+ (Jenny's-WF) 739 Media:TR-(JW-WF)-739-alignment.mas new version still w/ TR + Jenny's-WF Media:TR-(JW-WF)-739-alignmentedit.mas Tree of all 739 clones from TR Media:TR-739-tree.pdf Tree of TR + (Jenny's-WF) 739 Media: TR+(JW-WF)-739-tree.pdf new version still w/ TR + Jenny's-WF Media:TR + (JW-WF)-739-treeedit.pdf
Green Jesse 405 Media: TR-Green_405-C1.txt Media: TR-Green_405-C2.txt Media: TR-Green_405-C3-edit.txt Media: TR-Green_405-C4-edit.txt Media: TR-Green_405-C6-edit.txt Media: TR-Green_405-C7-edit.txt Media: TR-Green-405-Sepecies Overview.xlsx Media: WF-405_Alignment_with_TR_edited.mas Media: Phylogeny Tree TF and Steve only with edits to TR.pdf
Green
Blue
Blue Noa 702 Media:TR-Blue-702-C4.txt Media:TR-Blue-702-C5.txt Media:TR-Blue-702-C6.txt Media:TR-Blue-702-C8.txt Media:TR-Blue-702.xlsx Media:TR-Red-Blue-702.mas Media:TR-Blue-Red-tree.pdf
Pink Justin & Arturo 709 Media:TR-Pink_709-C5B.txt Media:TR-Pink_709-C6B.docx Media:TR-Pink_709B.xlsx
Pink 709 Media: B1.txt
Purple Sarah 739 Media:TR-Purple_739-C1.txt Media:TR-Purple_739-C2.txt Media:TR-Purple_739-C3.txt Media:TR-Purple_739-C4.txt Media:TR-Purple_739-C7.txt Media:TR-Purple_739-C8.txt Media:S13-M1D7-template-Sarah Yu.xlsx Media:module1.mas more complete file in Dominique's box
Purple Mitali 664 Media:TR-Purple_664-C2.txt Media:TR-Purple_664-C5.txt Media:TR-Purple_664-C7.txt Media:TR-Purple_664-C8.txt Media:TR-Purple_664-MK.xlsx Media: WFTR-664-alignment.mas Media: WFTR-664-tree.pdf
Platinum Emily 732 Media:TR_platinum_732_c2.txt Media:TR_platinum_732_c3.txt Media:TR_platinum_732_c4.txt Media:TR_platinum_732_c5.txt Media:TR_platinum_732.xlsx Media:emily and nikki m5 data.mas
Platinum Katie 405 Updated AGA start: Media:TR_Platinum_405_c1_edited.txt - Media:TR_Platinum_405_c3.txt - Media:TR_Platinum_405_c5.txt Media:TR_Platinum_405_c6.txt - Updated AGA start: Media:TR_Platinum_405_c8_edited.txt Media:KB_TR_Platinum.xlsx Katie before combining with Jesse: Media:KatieJesseSession.mas, Katie and Jesse (405) Aligned: Media: TR-405 alignment.mas, Katie, Jesse and Steve C. alignment: Media: WF-405 Alignment with TR edited.mas Katie and Jesse (405) finished tree - Media: TR-405-PhyloTree.pdf, Katie,Jesse Steve corrected tree (waiting on 4th 405 sample)- Media: 405 Phylogeny Tree TF and Steve only with edits to TR.pdf



W/F microbiome

Linking a file code: [[Media: filename.extension]] or optionally [[Media: filename.extension | description]].

Team Color Team Member Gull ID Sequence 1 (txt) Sequence 2 (txt) Sequence 3 (txt) Sequence 4 (txt) Sequence 5 (txt) Sequence 6 (txt) Sequence 7 (txt) Sequence 8 (txt) Species overview (xlsx) Alignment (mas) Tree (pdf)
Red Divya Arcot 702 Media: WF_RED_4,12.txt‎ Media: WF_RED_5,13.txt Media: WF_RED_6,14.txt‎‎ Media: WF_RED_7,15.txt Media: WF_RED_-_S13-M1D7-template.xlsx‎ Media: WF-Red,TR-Red-Blue-702.mas‎ Media: WF_Red,_TR_Red,Blue.pdf‎
Red Maria Escobar 702 Media: WF_red_702_17.txt‎ Media: WF_red_702_18.txt‎ Media: WF_red_702_20.txt‎ Media: WF_red_702_22.txt‎ Media: WF_red_702_23.txt Media: WF_red_702_24.txt‎ Media: WF-Red-702.xlsx‎
Orange Amelia Mockett 709 Media: WF-Orange_709-C1.txt Media: WF-Orange_709-C2.txt Media: WF-Orange_709-C5.txt Media: WF-Orange_709-C8.txt Media: S13-M1D7-WF-Orange-Mockett.xlsx
Orange Katie Gorick 712 Media: WF-Orange_712-C3.txt Media: WF-Orange_712-C4.txt Media: WF-Orange_712-C6.txt Media: WF-Orange_712-C8.txt Media: WF-Orange_712.xlsx Media: FULL 712 Alignment(TR_Orange + WF_Blue, Orange, Pink).mas Media: FULL 712 PhyloTree (TR_Orange + WF_Orange, Blue, Pink).pdf
Yellow Jenny Wei 739 Media: WF-Yellow_739-C1.txt Media: WF-Yellow_739-C3.txt Media: WF-Yellow_739-C4.txt Media: WF-Yellow_739-C5.txt Media: WF-Yellow_739-C7.txt Media: WF-Yellow_739-C8.txt Media: WF-Yellow_739.xlsx Media: WF-739-Alignment.mas Media: WF-739-Phylogenetic Tree.pdf
Yellow Karinna Vivanco 664 Media: WF-Yellow_664-C4.txt Media: WF-Yellow_664-C5.txt Media: WF-Yellow_664-C6.txt Media: WF-Yellow_664-C7.txt Media: WF-Yellow_664.xlsx WF-664-Alignment(+TR Purple).mas WF-664-Phylogenetic Tree(+TR Purple).pdf
Green Kevin Hu 732 Media: WF-Green_732-C4.txt Media: WF-Green_732-C5.txt Media: WF-Green_732-C7.txt Media: WF-Green_732.xlsx Media: WF-732 Alignment (TR-Platinum, WF-Green, Platinum).mas Media: WF-732-PhyloTree (TR-Platinum + WF-Green, Platinum).pdf
Green Steve Cho 405 Media: WF-Green_405-C1.txt Media: WF-Green_405-C3.txt Media: WF-Green_405-C7.txt Media: WF-Green_405.xlsx Media: WF-405 Alignment with TR edited.mas Media: 405 Phylogeny Tree TF and Steve only with edits to TR.pdf
Blue Emmanuel Carrodeguas 712 Media: WF-Blue_712-C1.txt Media: WF-Blue_712-C3.txt Media: WF-Blue_712-C4.txt Media: WF-Blue_712-C5.txt Media: WF-Blue_712-C7.txt Media: WF-Blue_712-C8.txt Media: WF-Blue_712.xlsx Media: WF-712-Alignment(WF_Blue+TR_Orange).mas Media: WF-712-Alignment(WF_Blue+TR_Orange).pdf
Blue Sachin Shinde 702 Media: WF-Blue_702-C7.txt Media: WF-Blue_702-C8.txt Media: WF-Blue_702.xlsx Media: WF-702-alignment(TR-Red,TR-Blu,WF-Red,WF-Blu).mas Media: WF-702-tree(TR-Red,TR-Blu,WF-Red,WF-Blu).pdf
Pink Alice Chen 712 Media: WF-Pink_712C4.txt Media: WF-Pink_712C5.txt Media: WF-Pink_712C6.txt Media: WF-Pink_712C7.txt Media: WF-Pink_712C8.txt Media: WF-Pink_712.xlsx Media: WF-712-Alignment(WF_Blue+TR_Orange+WF_Pink).mas
Pink Helen He 709 Media: WF-Pink_709-B1.txt Media: WF-Pink_709-B2.txt Media: WF-Pink_709-B3.txt Media: WF-Pink_709-B4.txt Media: WF-Pink_709-B6.txt Media: WF-Pink_709.xlsx Media: WF-709-Alignment.mas Media: WF-709-Alignment.pdf
Purple Jenny Van 664 Media: WF-Purple_664-C1.txt Media: WF-Purple_664-C2.txt Media: WF-Purple_664-C3.txt Media: WF-Purple_664-C4.txt Media: WF-Purple_664-C8.txt Media: WF-Purple_664.xlsx Media: WFTR-664-Alignment.mas Media: WRTF-664-tree.pdf
Purple Zeinab Aboud 739 Media: WF-Purple_739-c1.txt Media: WF-Purple_739-C2.txt Media: WF-Purple_739-C3.txt Media: WF-Purple_739-C5.txt Media: WF-Purple_739-C8.txt Media: WF-Purple_739.xlsx Media: FINAL-739MA-alignment.mas‎ Media: FINAL-739-Phylogenetic_Tree.pdf‎
Platinum Eric Klinkhammer 732 Media: plt-1.txt Media: 2.txt Media: 3.txt Media: 4.txt Media: 5.txt Media: 6.txt Media: plt-7.txt Media: 8.txt Media: WF_732_sequence_data.xlsx Media: WF-732 Alignment (TR-Platinum, WF-Green, Platinum).mas Media: WF-732-PhyloTree (TR-Platinum + WF-Green, Platinum).pdf
Platinum Shanthi Ravi 405 Media: WF-PLT_405-C2.txt Media: WF-PLT_405-C3.txt Media: WF-PLT_405-C4.txt Media: WF-PLT_405-C5.txt Media: WF-PLT_405-C7.txt Media: WF-PLT_405-C8.txt Media: WF-PLT_405.xlxs

T/R microsporidia gels

Gel 1
Gel 2, bright
Gel 3
Gel 4
Gel 2, dim -- not sure why image won't show


W/F microsporidia gels

Gel 2
Gel 3
Gel 4
Gel 1, bright
Gel 1, dim


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